Biodiversity conservation planning is highly important in the current context of global change. Biodiversity conservation can be achieved by understanding changes in land use at the landscape scale. Such understanding is needed to reverse the unprecedented pressure on natural resources that has been reported by many studies conducted on biodiversity conservation within the Oti-Keran-Mandouri protected areas. Land cover maps reflecting different dates (1987, 2000, and 2013) and depicting different management systems, with overall accuracy ranging from 73% to 79%, were analyzed to understand the processes that lead to habitat degradation within these protected areas. The nature of change, within a given land cover class, was determined by comparing land cover maps on different dates using a decision tree algorithm that compares the number of patches, their areas, and their perimeters at different time periods (T₁ and T₂). Specifically, two time-periods were considered for this analysis: 1987–2000 and 2000–2013. Croplands and settlements increased at an average of 108.13% and 5.45%, respectively, from 1987 to 2000. From 2000 to 2013, croplands gained from all other land categories and continued to increase at a rate of 11.77% per year, whereas forests and savannas decreased at an annual average rate by 5.79% and 2.32%, respectively. The dominant processes of habitat change from 1987 to 2000 were the creation of forests, dissection of savannas, attrition of wetlands, and creation of croplands. Meanwhile, from 2000 to 2013, there was attrition of forests, as well as attrition of savannas, dissection of wetlands, and aggregation of croplands. In general, from 1987 to 2013, natural habitats regressed and were replaced by croplands; forests, savannas, and wetlands decreased at an average annual percentage 5.74%, 3.94%, and 2.02%, respectively, whereas croplands increased at an average annual rate of 285.39% of their own area. Aggregation, attrition, dissection, and creation were the main habitat change processes identified for the overall period from 1987 to 2013. There was habitat loss in forests and savannas and habitat fragmentation in wetland due to attrition and dissection, respectively. Identifying and understanding habitat change processes would enable the taking of appropriate biodiversity conservation actions.